In immunocompromised patients, respiratory syncytial virus (RSV) infections are known to be severe and prolonged, and have significant mortality and morbidity. However, little is known about the clinical courses and treatment strategy of RSV infection in heart transplant recipients. Here, we report a 6-year-old female with heart transplantation who had exhibited prolonged respiratory symptoms and shedding of RSV. She had received everolimus as an immunosuppressant. As immunosuppressants could have been responsible for the prolonged activation of RSV, we converted everolimus to mycophenolate mofetil. After the conversion, RSV promptly disappeared, and her symptoms improved. We speculate that converting the immunosuppressant may be effective for prolonged RSV infection due to the different immunosuppressive mechanisms.